Had a great Sunday, biked to Santa Barbara with Michael and a few others from the course. Got some delicious tacos, and some nice ice cream too. Ended with barbeque and ping pong. Not a bad day off.

Second week is about to start. We’ll do some DNA extraction and sequencing later in the week, but until then I’ll look through the data. Thought I’d use this space to try to plan out what I want to do. I tend to feel a bit overwhelmed when first getting a new dataset, not knowing what to do first. Feel additionally stressed about this one, because we have a time constraint for the course, and I think I’m feeling a little more pressure/competetiveness to do something good. We’ll see how that turns out.

Overall the goal for this week is to get a bit more familiar with the data and

Visualizing the data

Guilhem, Paul Rainey’s grad student, had put together some nice visualizations of some of the sequencing data. I think my first goal is to recreate/extend that. What I want to do is make a script that does the following, given a particular dataset as input:

  • Gives me the overall average coverage and the distribution of coverage per contig/over the genome.
  • Histograms of mapping accuracy at different positions. One would think that we should get >90% accuracy of a match if a metagenome read really came from the same type; the errors should be dominated by the nucleotide errors of the original genome. We can use the timepoint where things came from to try to judge this.
  • Coverage cumulative distributions per nucleotide, averaged over a small window. Do this with different cutoffs (probably some kind of logarithmic scale) in order to get a sense of what the reads at different frequencies looks like.

In addition, if I have time I may want to make a data exploration tool which lets me load a file, put in a contig number and base pair range, and shows me a variety of these stats in that given window. We’ll see how long that would take to code/how useful that would be.

Evolutionary scenarios

By looking at the data with the above tools, we can try to falsify the various evolutionary scenarios which could have occured:

  • Individual was present at early times, didn’t fix until later ones. Here horizontal gene transfer within the bottle may have contributed to structural variation, but that/initial diversity dominated rather than transfer between bottles. Can check to see if gaps get filled in other bottles, if gaps get filled in the vertical treatment, and how correlated gaps are in different bottles.
  • Some individual(s) got transferred in from another bottle. Maybe some whole bacteria were transferred; they may be adpative in another condition, so got to high enough frequency to be transferred, and then got transferred wholesale to the new bottle. Would look for some conditions where all the gaps are filled, as well as correlation between gaps coming up.
  • Horizontal gene transfer of specific elements. The golden goose. Would want to show that some gaps get filled in, and that gaps don’t come at all from vertical conditions. Also need to find the junctions and show that they differ bottle to bottle.

Later analyses

Analyses I want to get to later in the week once I have a better sense of the data include:

Gap analysis. I want to try and come up with some way of identifying gaps, and classifying them. I need to use the coverage to compute a basic null expectation for how large gaps can be at random, as well as use the reads mapping on to their same timepoint to create two methods of finding the lengths of gaps which may be real. Can also use time course correlation as well. In addition need to write a simple average in window to actually find the ends of the gaps (all tunable).

Low frequency matches. Allowing for lower frequency matches may start filling in the gaps; maybe this could be used to try and figure out if, at low coverage/earlier timepoints when gaps are somewhat speckled, the filling is real or not.

Guessing at the evolutionary history of gaps. Using the above and the time course, can we say something about the origin of/evolutionary history of the gaps? This would be the ultimate goal.

Find reads which span the junctions. This would be good to see if, for example, when the gap gets filled in in other bottles whether or not it actually is incorporated in the same place, or if there are differences.